[sciurius]

I gave it a try.
I copied Some_Music.pdf as Foo.pdf and imported it ("Let MobileSheets Manage my Files" is off).
I made some annotations to Foo (Some Music) and back to the index list.
I copied Some_Other_Music.pdf as Foo.pdf and then selected "Foo" on the index list.
The new (Some Other Music) document shows, with the existing annotations at the original places. This is actually what I would expect to happen.
The same happens with "Swap file".
Since MobileSheetsPro registers file size and dates, it may be worth to check whether the physical file has been changed and notify the user that it will be reloaded.

PS: I would not be surprised if changing a file for a shorter one may confuse (crash) MSP so I assume "Swap file" would always be the preferred way to change a file.